| 1. |
- Sirami, Clélia, et al.
(författare)
-
Increasing crop heterogeneity enhances multitrophic diversity across agricultural regions
- 2019
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:33, s. 16442-16447
-
Tidskriftsartikel (refereegranskat)abstract
- Agricultural landscape homogenization has detrimental effects on biodiversity and key ecosystem services. Increasing agricultural landscape heterogeneity by increasing seminatural cover can help to mitigate biodiversity loss. However, the amount of seminatural cover is generally low and difficult to increase in many intensively managed agricultural landscapes. We hypothesized that increasing the heterogeneity of the crop mosaic itself (hereafter “crop heterogeneity”) can also have positive effects on biodiversity. In 8 contrasting regions of Europe and North America, we selected 435 landscapes along independent gradients of crop diversity and mean field size. Within each landscape, we selected 3 sampling sites in 1, 2, or 3 crop types. We sampled 7 taxa (plants, bees, butterflies, hoverflies, carabids, spiders, and birds) and calculated a synthetic index of multitrophic diversity at the landscape level. Increasing crop heterogeneity was more beneficial for multitrophic diversity than increasing seminatural cover. For instance, the effect of decreasing mean field size from 5 to 2.8 ha was as strong as the effect of increasing seminatural cover from 0.5 to 11%. Decreasing mean field size benefited multitrophic diversity even in the absence of seminatural vegetation between fields. Increasing the number of crop types sampled had a positive effect on landscape-level multitrophic diversity. However, the effect of increasing crop diversity in the landscape surrounding fields sampled depended on the amount of seminatural cover. Our study provides large-scale, multitrophic, cross-regional evidence that increasing crop heterogeneity can be an effective way to increase biodiversity in agricultural landscapes without taking land out of agricultural production.
|
|
| 2. |
- Alignier, Audrey, et al.
(författare)
-
Configurational crop heterogeneity increases within-field plant diversity
- 2020
-
Ingår i: Journal of Applied Ecology. - : Wiley. - 0021-8901 .- 1365-2664. ; 57:4, s. 654-663
-
Tidskriftsartikel (refereegranskat)abstract
- Increasing landscape heterogeneity by restoring semi-natural elements to reverse farmland biodiversity declines is not always economically feasible or acceptable to farmers due to competition for land. We hypothesized that increasing the heterogeneity of the crop mosaic itself, hereafter referred to as crop heterogeneity, can have beneficial effects on within-field plant diversity. Using a unique multi-country dataset from a cross-continent collaborative project covering 1,451 agricultural fields within 432 landscapes in Europe and Canada, we assessed the relative effects of compositional and configurational crop heterogeneity on within-field plant diversity components. We also examined how these relationships were modulated by the position within the field. We found strong positive effects of configurational crop heterogeneity on within-field plant alpha and gamma diversity in field interiors. These effects were as high as the effect of semi-natural cover. In field borders, effects of crop heterogeneity were limited to alpha diversity. We suggest that a heterogeneous crop mosaic may overcome the high negative impact of management practices on plant diversity in field interiors, whereas in field borders, where plant diversity is already high, landscape effects are more limited. Synthesis and applications. Our study shows that increasing configurational crop heterogeneity is beneficial to within-field plant diversity. It opens up a new effective and complementary way to promote farmland biodiversity without taking land out of agricultural production. We therefore recommend adopting manipulation of crop heterogeneity as a specific, effective management option in future policy measures, perhaps adding to agri-environment schemes, to contribute to the conservation of farmland plant diversity.
|
|
| 3. |
- Austrell, P. E., et al.
(författare)
-
Extending the visco-frictional branched modeling of filled rubbers to include coupling effects between rate and amplitude dependence
- 2019. - 1
-
Ingår i: Constitutive Models for Rubber XI : Proceedings of the 11th European Conference on Constitutive Models for Rubber, 2019 - Proceedings of the 11th European Conference on Constitutive Models for Rubber, 2019. - : CRC Press. - 9780367342586 - 9780429324710 ; , s. 267-272
-
Konferensbidrag (refereegranskat)abstract
- The traditional way to capture rate and amplitude dependence of filled rubbers is by a branched model containing elastic, viscous, and frictional branches, leading to a decoupling of the rate and amplitude dependence. In order to capture the experimentally observed phenomena with a steeper increasing dynamic modulus with frequency, for small amplitudes, a model by Besseling (1958) is revisited. In it‘s general form several stress fractions are added and each fraction has elastic, viscous, and frictional contributions in series. In this work the potential of Bessling‘s constitutive model is investigated by extending the traditional three branches by a forth branch from this model to account for the coupling effects. The stress calculation algorithms and behavior of one-dimensional models are compared to harmonic experiments in double shear. A simple eight parameter model is studied and shown roughly to give the desired behavior, although no fitting routine has been implemented.
|
|
| 4. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
-
Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
- 2013
-
Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
-
Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
|
|
| 5. |
- Bertrand, Yann, et al.
(författare)
-
Assignment of homoeologues to parental genomes in allopolyploids for species tree inference, with an example from Fumaria (Papaveraceae)
- 2015
-
Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 64:3, s. 448-471
-
Tidskriftsartikel (refereegranskat)abstract
- There is a rising awareness that species trees are best inferred from multiple loci while taking into account processes affecting individual gene trees, such as substitution model error (failure of the model to account for the complexity of the data) and coalescent stochasticity (presence of incomplete lineage sorting). Although most studies have been carried out in the context of dichotomous species trees, these processes operate also in more complex evolutionary histories involving multiple hybridizations and polyploidy. Recently, methods have been developed that accurately handle incomplete lineage sorting in allopolyploids, but they are thus far restricted to networks of diploids and tetraploids. We propose a procedure that improves on this limitation by designing a workflow that assigns homoeologues to hypothetical diploid ancestral genomes prior to genome tree construction. Conflicting assignment hypotheses are evaluated against substitution model error and coalescent stochasticity. Incongruence that cannot be explained by stochastic mechanisms needs to be explained by other processes (e.g., homoploid hybridization or paralogy). The data can then be filtered to build multilabeled genome phylogenies using inference methods that can recover species trees, either in the face of substitution model error and coalescent stochasticity alone, or while simultaneously accounting for hybridization. Methods are already available for folding the resulting multilabeled genome phylogeny into a network. We apply the workflow to the reconstruction of the reticulate phylogeny of the plant genus Fumaria (Papaveraceae) with ploidal levels ranging from 2x to 14x. We describe the challenges in recovering nuclear NRPB2 homoeologues in high ploidy species while combining in vivo cloning and direct sequencing techniques. Using parametric bootstrapping simulations we assign nuclear homoeologues and chloroplast sequences (four concatenated loci) to their common hypothetical diploid ancestral genomes. As these assignments hinge on effective population size assumptions, we investigate how varying these assumptions impacts the recovered multilabeled genome phylogeny.
|
|
| 6. |
|
|
| 7. |
- Bertrand, Yann, et al.
(författare)
-
First Dating of a Recombination Event in Mammalian Tick-borne Flaviviruses
- 2012
-
Ingår i: PLoS ONE. - San Francisco : Public Library of Science (PLoS). - 1932-6203. ; 7:2
-
Tidskriftsartikel (refereegranskat)abstract
- The mammalian tick-borne flavivirus group (MTBFG) contains viruses associated with important human and animal diseases such as encephalitis and hemorrhagic fever. In contrast to mosquito-borne flaviviruses where recombination events are frequent, the evolutionary dynamic within the MTBFG was believed to be essentially clonal. This assumption was challenged with the recent report of several homologous recombinations within the Tick-borne encephalitis virus (TBEV). We performed a thorough analysis of publicly available genomes in this group and found no compelling evidence for the previously identified recombinations. However, our results show for the first time that demonstrable recombination (i.e., with large statistical support and strong phylogenetic evidences) has occurred in the MTBFG, more specifically within the Louping ill virus lineage. Putative parents, recombinant strains and breakpoints were further tested for statistical significance using phylogenetic methods. We investigated the time of divergence between the recombinant and parental strains in a Bayesian framework. The recombination was estimated to have occurred during a window of 282 to 76 years before the present. By unravelling the temporal setting of the event, we adduce hypotheses about the ecological conditions that could account for the observed recombination.
|
|
| 8. |
|
|
| 9. |
|
|
| 10. |
- Bertrand, Yann J., et al.
(författare)
-
Revisiting Recombination Signal in the Tick-Borne Encephalitis Virus : A Simulation Approach
- 2016
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:10
-
Tidskriftsartikel (refereegranskat)abstract
- The hypothesis of wide spread reticulate evolution in Tick-Borne Encephalitis virus (TBEV) has recently gained momentum with several publications describing past recombination events involving various TBEV clades. Despite a large body of work, no consensus has yet emerged on TBEV evolutionary dynamics. Understanding the occurrence and frequency of recombination in TBEV bears significant impact on epidemiology, evolution, and vaccination with live vaccines. In this study, we investigated the possibility of detecting recombination events in TBEV by simulating recombinations at several locations on the virus' phylogenetic tree and for different lengths of recombining fragments. We derived estimations of rates of true and false positive for the detection of past recombination events for seven recombination detection algorithms. Our analytical framework can be applied to any investigation dealing with the difficult task of distinguishing genuine recombination signal from background noise. Our results suggest that the problem of false positives associated with low detection P-values in TBEV, is more insidious than generally acknowledged. We reappraised the recombination signals present in the empirical data, and showed that reliable signals could only be obtained in a few cases when highly genetically divergent strains were involved, whereas false positives were common among genetically similar strains. We thus conclude that recombination among wild-type TBEV strains may occur, which has potential implications for vaccination with live vaccines, but that these events are surprisingly rare.
|
|
| 11. |
- Bertrand, Yann, et al.
(författare)
-
Phylogenetic hypotheses, taxonomic sameness and the reference of taxon names
- 2008
-
Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 37:3, s. 337-347
-
Tidskriftsartikel (refereegranskat)abstract
- When scientists use a taxon name like Mammalia, it is important that they talk about the same thing. But, what does it mean to be the same thing in different phylogenetic hypotheses? And, how is taxonomic reference maintained across hypotheses? Here, we discuss the differences between real and hypothetical clades, and how such a distinction relates to the sameness problem. Since hypotheses influence how we perceive things and pursue science, we find it important to have a functioning nomenclatural system for clades as perceived in phylogenetic hypotheses. As a solution to the sameness problem for such clades, we argue that a taxon name does not primarily refer to a single clade that somehow mirror the reality of branches in the tree of life. Instead we suggest that a taxon name refers to a set, or natural kind, of counterfactual and reconstructed clades.
|
|
| 12. |
- Bertrand, Yann
(författare)
-
Relationships between nomenclature, phylogenetics and systematics
- 2008
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Systematists have become increasingly aware of the limits imposed by the current system of nomenclature for accurately representing evolutionary relationships and managing efficiently names associated with clades. In reaction, a new system of nomenclature, the PhyloCode is being developed that fully recognizes the historical nature of taxonomy and the importance of the cladistics revolution. As a consequence, questions emerge about the new historical entities of systematics, questions that can be apprehended through the lens of epistemology, philosophy of language and metaphysics. What is the ontological nature of entities that lack any other essential features besides spatiotemporal properties? How to depart from the fixed realm of immutable and transcendental essence into a worldview wherein all biological entities are characterized by their temporality and materiality? What are the consequences of nomenclatural decisions on other sectors of biology? With the ever growing sequencing capacity and tree reconstructing abilities, our conceptualization of phylogenetic relationships is changing at an unprecedented pace. Then it begs the question, what prevents communication break down when the references of clades’ names are changing almost on a daily basis. These are some of the fundamental issues I am tackling in the present work. Addressing the ontological issue, I argue that species and clades are best perceived as mereological sums of individuals, which means that each biological individual is the unique individual composed of all its less inclusive individuals and nothing more. I propose to separate the meanings of “clade” and “monophyletic group”. I suggest to use “monophyletic” for an epithet referring to a defining property of a set (a natural kind) and “clade” for a noun which corresponds to a historical entity (an individual) resulting from evolutionary process. I present the idea that a phyloname is not attached to a single clade but to a natural kind containing as members the clades that would be selected in counterfactual phylogenies. The defining properties of this natural kind are provided by the phylogenetic definition. Finally I stress that taxonomists are also driven by the will to narrate the same sort of history, when they adjust the reference of names in light of new phylogenetic data, which leads me to submit that taxa can also be perceived as narratives.
|
|
| 13. |
|
|
| 14. |
|
|
| 15. |
- Bertrand, Yann, et al.
(författare)
-
Taxonomic surrogacy in biodiversity assessments, and the meaning of Linnaean ranks
- 2006
-
Ingår i: Systematics and Biodiversity. ; 4:2, s. 149-159
-
Tidskriftsartikel (refereegranskat)abstract
- The majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the relationships between taxa and ranks, and suggest that species/higher taxon exchanges are founded on misconceptions about the properties of Linnaean classification. Rank allocations in current classifications constitute a heterogeneous mixture of various historical and contemporary views. Even if all taxa were monophyletic, those referred to the same rank would simply denote separate clades without further equivalence. We conclude that they are no more comparable than any other, non-nested taxa, such as, for example, the genus Rattus and the phylum Arthropoda, and that taxonomic surrogacy lacks justification. These problems are also illustrated with data of polychaetous annelid worms from a broad-scale study of benthic biodiversity and species distributions in the Irish Sea. A recent consensus phylogeny for polychaetes is used to provide three different family-level classifications of polychaetes. We use families as a surrogate for species, and present Shannon–Wiener diversity indices for the different sites and the three different classifications, showing how the diversity measures rely on subjective rank allocations
|
|
| 16. |
- Blanco-Pastor, José Luis, et al.
(författare)
-
Evolutionary networks from RADseq loci point to hybrid origins of Medicago carstiensis and Medicago cretacea
- 2019
-
Ingår i: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 106:9, s. 1219-1228
-
Tidskriftsartikel (refereegranskat)abstract
- Premise Although hybridization has played an important role in the evolution of many plant species, phylogenetic reconstructions that include hybridizing lineages have been historically constrained by the available models and data. Restriction-site-associated DNA sequencing (RADseq) has been a popular sequencing technique for the reconstruction of hybridization in the next-generation sequencing era. However, the utility of RADseq for the reconstruction of complex evolutionary networks has not been thoroughly investigated. Conflicting phylogenetic relationships in the genus Medicago have been mainly attributed to hybridization, but the specific hybrid origins of taxa have not been yet clarified. Methods We obtained new molecular data from diploid species of Medicago section Medicago using single-digest RADseq to reconstruct evolutionary networks from gene trees, an approach that is computationally tractable with data sets that include several species and complex hybridization patterns. Results Our analyses revealed that assembly filters to exclusively select a small set of loci with high phylogenetic information led to the most-divergent network topologies. Conversely, alternative clustering thresholds or filters on the number of samples per locus had a lower impact on networks. A strong hybridization signal was detected for M. carstiensis and M. cretacea, while signals were less clear for M. rugosa, M. rhodopea, M. suffruticosa, M. marina, M. scutellata, and M. sativa. Conclusions Complex network reconstructions from RADseq gene trees were not robust under variations of the assembly parameters and filters. But when the most-divergent networks were discarded, all remaining analyses consistently supported a hybrid origin for M. carstiensis and M. cretacea.
|
|
| 17. |
- Cousyn, Louis, et al.
(författare)
-
Brain MRI features and scoring of leukodystrophy in adult-onset Krabbe disease
- 2019
-
Ingår i: Neurology. - : Lippincott Williams & Wilkins. - 0028-3878 .- 1526-632X. ; 93:7, s. E647-E652
-
Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: To perform a systematic analysis and scoring of brain MRI white matter hyperintensities (WMH) in adult-onset Krabbe disease.METHODS: We retrospectively collected basic clinical data and the first available brain MRI from patients with confirmed Krabbe disease with first clinical manifestations beyond 10 years of age. Data were obtained from our reference center for lysosomal diseases (n = 6) and from contacted authors of published articles describing patients with adult-onset Krabbe disease (n = 15). T2-weighted fluid-attenuated inversion recovery images of each patient were analyzed and scored using a radiologic score of WMH in a single center.RESULTS: The corticospinal tract was always affected by WMH (100% of patients), however, with some distinctions along the tract: the precentral gyrus (100%), corona radiata (95%), and posterior internal capsule (81%) were highly abnormal, whereas the mesencephalon (57%), pons (52%), and medulla oblongata (5%) were less affected. WMH were also frequently present in the posterior lateral periventricular white matter (95%), optic radiations (86%), postcentral gyrus (71%), medial lemniscus (62%), and corpus callosum, especially in the isthmus (71%), whereas the genu was always normal. A few patients did not have the classical MRI pattern but extensive hyperintensities (n = 3), or patchy distribution of hyperintensities mimicking an acquired etiology (n = 2), or very subtle hyperintensities of the corticospinal tract (n = 1).CONCLUSIONS: We specified the main locations of WMH, which were observed in the earliest stages of the disease and were also present in patients with atypical MRI pattern, highlighting the importance of radiologic features to guide the diagnosis.
|
|
| 18. |
- de Sousa, Filipe, et al.
(författare)
-
Chloroplast genome and nuclear loci data for 71 Medicago species
- 2024
-
Ingår i: DATA IN BRIEF. - 2352-3409. ; 54
-
Tidskriftsartikel (refereegranskat)abstract
- We present a dataset containing nuclear and chloroplast sequences for 71 species in genus Medicago (Fabaceae), as well as for 8 species in genera Melilotus and Trigonella . Sequence data for a total of 130 samples was obtained with high-throughput sequencing of enriched genomic DNA libraries targeting 61 single-copy nuclear genes from across the Medicago truncatula genome. Chloroplast sequence reads were also generated, allowing for the recovery of chloroplast genome sequences for all 130 samples. A fully-resolved phylogenetic tree was inferred from the chloroplast dataset using maximum-likelihoood methods. More than 80% of accepted Medicago species are represented in this dataset, including three subspecies of Medicago sativa (alfalfa). These data can be further utilised for phylogenetic analyses in Medicago and related genera, but also for probe and primer design and plant breeding studies.
|
|
| 19. |
- Elväng, Annelie, et al.
(författare)
-
Sequencing of a Tick-Borne Encephalitis Virus from Ixodes ricinus Reveals a Thermosensitive RNA Switch Significant for Virus Propagation in Ectothermic Arthropods
- 2011
-
Ingår i: Vector Borne and Zoonotic Diseases. - : Mary Ann Liebert Inc. - 1530-3667 .- 1557-7759. ; 11:6, s. 649-658
-
Tidskriftsartikel (refereegranskat)abstract
- Tick-borne encephalitis virus (TBEV) is a flavivirus with major impact on global health. The geographical TBEV distribution is expanding, thus making it pivotal to further characterize the natural virus populations. In this study, we completed the earlier partial sequencing of a TBEV pulled out of a pool of RNA extracted from 115 ticks collected on Torö in the Stockholm archipelago. The total RNA was sufficient for all sequencing of a TBEV genome (Torö-2003), without conventional enrichment procedures such as cell culturing or suckling mice amplification. To our knowledge, this is the first time that the genome of TBEV has been sequenced directly from an arthropod reservoir. The Torö-2003 sequence has been characterized and compared with other TBE viruses. In silico analyses of secondary RNA structures formed by the two untranslated regions revealed a temperature-sensitive structural shift between a closed replicative form and an open AUG accessible form, analogous to a recently described bacterial thermoswitch. Additionally, novel phylogenetic conserved structures were identified in the variable part of the 3′-untranslated region, and their sequence and structure similarity when compared with earlier identified structures suggests an enhancing function on virus replication and translation. We propose that the thermo-switch mechanism may explain the low TBEV prevalence often observed in environmentally sampled ticks. Finally, we were able to detect variations that help in the understanding of virus adaptations to varied environmental temperatures and mammalian hosts through a comparative approach that compares RNA folding dynamics between strains with different mammalian cell passage histories.
|
|
| 20. |
- Eriksson, Jonna S., 1989, et al.
(författare)
-
A cryptic species produced by autopolyploidy and subsequent introgression involving Medicago prostrata (Fabaceae)
- 2017
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 107, s. 367-381
-
Tidskriftsartikel (refereegranskat)abstract
- Although hybridisation through genome duplication is well known, hybridisation without genome duplication (homoploid hybrid speciation, HHS) is not. Few well-documented cases have been reported. A possible instance of HHS in Medicago prostrata Jacq. was suggested previously, based on only two genes and one individual. We tested whether this species was formed through HHS by sampling eight nuclear loci and 22 individuals, with additional individuals from related species, using gene capture and Illumina sequencing. Phylogenetic inference and coalescent simulations were performed to infer the causes of gene tree incongruence. We found no evidence that phylogenetic differences among M. prostrata individuals were the result of HHS. Instead, an autopolyploid origin of tetraploids with introgression from tetraploids of the M. sativa complex is likely. We argue that tetraploid M. prostrata individuals constitute a new species, characterised by a partially non-overlapping distribution and distinctive alleles (from the M. sativa complex). No gene flow from tetraploid to diploid M. prostrata is apparent, suggesting partial reproductive isolation. Thus, speciation via autopolyploidy appears to have been reinforced by introgression. This raises the intriguing possibility that introgressed alleles may be responsible for the increased range exploited by tetraploid M. prostrata with respect to that of the diploids.
|
|
| 21. |
- Eriksson, Jonna S., 1989, et al.
(författare)
-
Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)
- 2018
-
Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 18:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Whole genome duplication plays a central role in plant evolution. There are two main classes of polyploid formation: autopolyploids which arise within one species by doubling of similar homologous genomes; in contrast, allopolyploidy (hybrid polyploidy) arise via hybridization and subsequent doubling of nonhomologous (homoeologous) genomes. The distinction between polyploid origins can be made using gene phylogenies, if alleles from each genome can be correctly retrieved. We examined whether two closely related tetraploid Mediterranean shrubs (Medicago arborea and M. strasseri) have an allopolyploid origin - a question that has remained unsolved despite substantial previous research. We sequenced and analyzed ten low-copy nuclear genes from these and related species, phasing all alleles. To test the efficacy of allele phasing on the ability to recover the evolutionary origin of polyploids, we compared these results to analyses using unphased sequences. Results: In eight of the gene trees the alleles inferred from the tetraploids formed two clades, in a non-sister relationship. Each of these clades was more closely related to alleles sampled from other species of Medicago, a pattern typical of allopolyploids. However, we also observed that alleles from one of the remaining genes formed two clades that were sister to one another, as is expected for autopolyploids. Trees inferred from unphased sequences were very different, with the tetraploids often placed in poorly supported and different positions compared to results obtained using phased alleles. Conclusions: The complex phylogenetic history of M. arborea and M. strasseri is explained predominantly by shared allotetraploidy. We also observed that an increase in woodiness is correlated with polyploidy in this group of species and present a new possibility that woodiness could be a transgressive phenotype. Correctly phased homoeologues are likely to be critical for inferring the hybrid origin of allopolyploid species, when most genes retain more than one homoeologue. Ignoring homoeologous variation by merging the homoeologues can obscure the signal of hybrid polyploid origins and produce inaccurate results. © 2018 The Author(s).
|
|
| 22. |
- Hass, Annika L., et al.
(författare)
-
Landscape configurational heterogeneity by small-scale agriculture, not crop diversity, maintains pollinators and plant reproduction in western Europe
- 2018
-
Ingår i: Proceedings of the Royal Society B: Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 285:1872
-
Tidskriftsartikel (refereegranskat)abstract
- Agricultural intensification is one of the main causes for the current biodiversity crisis. While reversing habitat loss on agricultural land is challenging, increasing the farmland configurational heterogeneity (higher field border density) and farmland compositional heterogeneity (higher crop diversity) has been proposed to counteract some habitat loss. Here, we tested whether increased farmland configurational and compositional heterogeneity promote wild pollinators and plant reproduction in 229 landscapes located in four major western European agricultural regions. High-field border density consistently increased wild bee abundance and seed set of radish (Raphanus sativus), probably through enhanced connectivity. In particular, we demonstrate the importance of crop-crop borders for pollinator movement as an additional experiment showed higher transfer of a pollen analogue along crop-crop borders than across fields or along semi-natural crop borders. By contrast, high crop diversity reduced bee abundance, probably due to an increase of crop types with particularly intensive management. This highlights the importance of crop identity when higher crop diversity is promoted. Our results show that small-scale agricultural systems can boost pollinators and plant reproduction. Agri-environmental policies should therefore aim to halt and reverse the current trend of increasing field sizes and to reduce the amount of crop types with particularly intensive management.
|
|
| 23. |
- Hyde, Kevin D., et al.
(författare)
-
Incorporating molecular data in fungal systematics: a guide for aspiring researchers
- 2013
-
Ingår i: Current Research in Environmental and Applied Mycology. - : Mushroom Research Foundation. - 2229-2225. ; 3:1
-
Tidskriftsartikel (refereegranskat)abstract
- The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching changes as disciplines in the wake of continual improvement in DNA sequencing technology. A taxonomic study that draws from molecular data involves a long series of steps, ranging from taxon sampling through the various laboratory procedures and data analysis to the publication process. All steps are important and influence the results and the way they are perceived by the scientific community. The present paper provides a reflective overview of all major steps in such a project with the purpose to assist research students about to begin their first study using DNA-based methods. We also take the opportunity to discuss the role of taxonomy in biology and the life sciences in general in the light of molecular data. While the best way to learn molecular methods is to work side by side with someone experienced, we hope that the present paper will serve to lower the learning threshold for the reader.
|
|
| 24. |
- Lopes de Abreu, Narjara, et al.
(författare)
-
The use of chloroplast genome sequences to solve phylogenetic incongruences in Polystachya Hook (Orchidaceae Juss)
- 2018
-
Ingår i: Peerj. - : PeerJ. - 2167-8359. ; 6
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Current evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or next generation sequencing (NGS) are an alternative to traditional methods that allow access to hundreds of DNA regions. Here we use this approach to resolve the phylogenetic incongruence found in Polystachya Hook. (Orchidaceae), a genus that stands out due to several interesting aspects, including cytological (polyploid and diploid species), evolutionary (reticulate evolution) and biogeographical (species widely distributed in the tropics and high endemism in Brazil). The genus has a notoriously complicated taxonomy, with several sections that are widely used but probably not monophyletic. Methods: We generated the complete plastid genome of 40 individuals from one clade within the genus. The method consisted in construction of genomic libraries, hybridization to RNA probes designed from available sequences of a related species, and subsequent sequencing of the product. We also tested how well a smaller sample of the plastid genome would perform in phylogenetic inference in two ways: by duplicating a fast region and analyzing multiple copies of this dataset, and by sampling without replacement from all non-coding regions in our alignment. We further examined the phylogenetic implications of non-coding sequences that appear to have undergone hairpin inversions (reverse complemented sequences associated with small loops). Results: We retrieved 131,214 bp, including coding and non-coding regions of the plastid genome. The phylogeny was able to fully resolve the relationships among all species in the targeted clade with high support values. The first divergent species are represented by African accessions and the most recent ones are among Neotropical species. Discussion: Our results indicate that using the entire plastid genome is a better option than screening highly variable markers, especially when the expected tree is likely to contain many short branches. The phylogeny inferred is consistent with the proposed origin of the genus, showing a probable origin in Africa, with later dispersal into the Neotropics, as evidenced by a clade containing all Neotropical individuals. The multiple positions of Polystachya concreta (Jacq.) Garay & Sweet in the phylogeny are explained by allotetraploidy. Polystachya estrellensis Rchb.f. can be considered a genetically distinct species from P. concreta and P. foliosa (Lindl.) Rchb.f., but the delimitation of P. concreta remains uncertain. Our study shows that NGS provides a powerful tool for inferring relationships at low taxonomic levels, even in taxonomically challenging groups with short branches and intricate morphology.
|
|
| 25. |
- Moazzeni, Hamid, et al.
(författare)
-
Phylogenetic perspectives on diversification, biogeography and character evolution in the species-rich genus Erysimum (Erysimeae; Brassicaceae) based on a densely sampled ITS approach
- 2014
-
Ingår i: Botanical journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4074 .- 1095-8339. ; 175:4, s. 497-522
-
Tidskriftsartikel (refereegranskat)abstract
- Erysimum includes 150–350 species distributed in the Northern Hemisphere, with Eurasia being the centre of greatest diversity. It is well known for its taxonomic complexity as a result of overlapping morphological characters. We present the first densely sampled phylogenetic analysis of Erysimum using internal transcribed spacer (ITS) DNA sequences from c. 85% of the species (117 for the first time), representing the full range of morphological variation and geographical distribution. We used several approaches to reconstruct phylogenetic relationships, dating of diversification and patterns of evolution of morphological characters in the genus. Ancestral-state reconstructions of four morphological diagnostic characters were performed using maximum parsimony, maximum likelihood and Bayesian methods. Our phylogenetic framework strongly supports the monophyly of Erysimum and recovers some well-supported clades that are geographically, rather than morphologically, correlated. Our study confirms the placement of Erysimum in lineage I and reveals two Malcolmia spp. (M.maritima and M.orsiniana) as its sister taxa. The results suggest that the biennial duration and caespitose habit (vs. annual or perennial duration and herbaceous or woody habit) and large, yellow, glabrous (vs. small, non-yellow, pubescent) petals are ancestral in Erysimum. The ancestral-state reconstruction results show that annual vs. perennial and woody vs. herbaceous features have been independently derived several times. The dating analyses suggest an early radiation of Erysimum during the late Pliocene or early Pleistocene.
|
|
| 26. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
-
A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation
- 2011
-
Ingår i: Mycoscience. - : The Mycological Society of Japan. - 1340-3540 .- 1618-2545. ; 52:4, s. 278-282
-
Tidskriftsartikel (refereegranskat)abstract
- Reverse complementary DNA sequences––sequences that are inadvertently cast backward and in which all purines and pyrimidines are transposed––are not uncommon in sequence databases, where they may introduce noise into sequence-based research. We show that about 1% of the public fungal ITS sequences, the most commonly sequenced genetic marker in mycology, are reverse complementary, and we introduce an open source software solution to automate their detection and reorientation. The MacOSX/Linux/UNIX software operates on public or private datasets of any size, although some 50 base pairs of the 5.8S gene of the ITS region are needed for the analysis.
|
|
| 27. |
- Pirani, Atefeh, et al.
(författare)
-
Molecular phylogeny of Acanthophyllum (Caryophyllaceae, Caryophylleae), with emphasis on infrageneric classification
- 2014
-
Ingår i: Taxon. - 0040-0262. ; 63:3, s. 592-607
-
Tidskriftsartikel (refereegranskat)abstract
- Despite being one of the larger genera of Caryophyllaceae with about 60 cushion-forming subshrubby species, Acanthophyllum is represented poorly in previous molecular phylogenetic studies. The genus is an important component of the subalpine steppe flora in Central to Southwest Asia. Although the placement of Acanthophyllum in the tribe Caryophylleae and a close relationship to Allochrusa has already been suggested, the monophyly of the genus and its infrageneric taxa, as well as its relation to other closely related genera, have not been addressed. We have assembled datasets of nuclear ribosomal internal transcribed spacer (ITS) sequences and intron sequences of the chloroplast gene rps16 for 47 Acanthophyllum species and 63 species of 11 additional genera from Caryophylleae. Phylogenetic analyses were performed using maximum parsimony, maximum likelihood and Bayesian methods. Our analysis suggests that Allochrusa, Diaphanoptera, Ochotonophila and Scleranthopsis are nested within Acanthophyllum but that the traditionally recognized sections of Acanthophyllum are monophyletic after reassignment of a few species. Emarginate petals may be a synapomorphy for one of the two basal clades of Acanthophyllum. Moreover, non-monophyly of the genera Gypsophila and Diaphanoptera is suggested by the present study. The age of the crown clade of Acanthophyllum s.l. is estimated to be 11.1 Ma by *BEAST species tree analysis.
|
|
| 28. |
- Sousa, Filipe de, 1982, et al.
(författare)
-
Patterns of phylogenetic incongruence in Medicago found among six linkage groups
- 2016
-
Ingår i: Plant Systematics and Evolution. - : Springer Science and Business Media LLC. - 0378-2697 .- 1615-6110 .- 2199-6881. ; 302:5, s. 493-513
-
Tidskriftsartikel (refereegranskat)abstract
- The species phylogeny of Medicago L. (Leguminosae) remains unresolved, as there is significant incongruence between the published gene phylogenies. Here, we compare six of these gene phylogenies of Medicago, inferred from unlinked loci from the nuclear, chloroplast and mitochondrial genomes. Data from all loci were re-analysed, including gap-coding of initial data sets, and dated phylogenies were produced. The patterns of species relationships observed in the six dated phylogenies are compatible with several different biological processes, such as incomplete lineage sorting and hybridisation. A subset of the original sampling that included 29 taxa was also analysed using coalescent-based tree distance comparisons. The observed topological distances suggest that differences between gene phylogenies cannot be solely attributed to incomplete lineage sorting. Hybridisation is strongly suspected to have occurred in the history of many taxa in the genus, because of overlapping divergence times between suspected hybrids and each parental lineage, confirming earlier results based on only two genes. An attempt to reconcile the conflicting histories in a multispecies coalescent analysis, using multiple labels for taxa with hybrid histories, did not produce satisfactory results and may be fatally limited. We conclude that although the currently available data are not sufficient to clarify relationships in Medicago, many cases of hybridisation are probable. The phylogenetic history of the genus is therefore better understood as a network and not a single tree. This raises concerns over previous studies that have used single gene trees as summaries of the history of species relationships.
|
|
| 29. |
- Sousa, Filipe de, 1982, et al.
(författare)
-
Phylogenetic properties of 50 nuclear loci in Medicago (Leguminosae) generated using multiplexed sequence capture and next-generation sequencing
- 2014
-
Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:10
-
Tidskriftsartikel (refereegranskat)abstract
- Next-generation sequencing technology has increased the capacity to generate molecular data for plant biological research, including phylogenetics, and can potentially contribute to resolving complex phylogenetic problems. The evolutionary history of Medicago L. (Leguminosae: Trifoliae) remains unresolved due to incongruence between published phylogenies. Identification of the processes causing this genealogical incongruence is essential for the inference of a correct species phylogeny of the genus and requires that more molecular data, preferably from low-copy nuclear genes, are obtained across different species. Here we report the development of 50 novel LCN markers in Medicago and assess the phylogenetic properties of each marker. We used the genomic resources available for Medicago truncatula Gaertn., hybridisation-based gene enrichment (sequence capture) techniques and Next-Generation Sequencing to generate sequences. This alternative proves to be a cost-effective approach to amplicon sequencing in phylogenetic studies at the genus or tribe level and allows for an increase in number and size of targeted loci. Substitution rate estimates for each of the 50 loci are provided, and an overview of the variation in substitution rates among a large number of low-copy nuclear genes in plants is presented for the first time. Aligned sequences of major species lineages of Medicago and its sister genus are made available and can be used in further probe development for sequence-capture of the same markers.
|
|
| 30. |
- Sousa, Filipe de, 1982, et al.
(författare)
-
Using genomic location and coalescent simulation to investigate gene tree discordance in Medicago L.
- 2017
-
Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 66:6, s. 934-949
-
Tidskriftsartikel (refereegranskat)abstract
- Several well-documented evolutionary processes are known to cause conflict between species-level phylogenies and gene-level phylogenies. Three of the most challenging processes for species tree inference are incomplete lineage sorting, hybridization and gene duplication, which may result in unwarranted comparisons of paralogous genes. Several existing methods have dealt with these processes but none has yet been able to untangle all three at once. Here, we propose a stepwise method by which these processes can be discerned using information on genomic location coupled with coalescent simulations. In the first step, highly discordant genes within genomic blocks (putative paralogs) are identified and excluded from the data set and, in the second step, blocks of linked genes are grouped according to their hybrid history. Existing multispecies coalescent software can then be applied to recover the principal tree(s) that make up the species tree/network without violating the underlying model. The potential of the approach is evaluated on simulated data derived from a species network composed of nine species, of which one is of hybrid origin, and displaying a single-gene duplication that leads to paralogous comparisons. We apply our method to an empirical set of 12 genes from 7 species sampled in the plant genus Medicago that display phylogenetic discordance. We identify the causes of the discordance and demonstrate that the Medicago orbicularis lineage experienced an episode of ancient hybridization. Our results show promise as a new way to explore phylogenetic sequence data that can significantly improve species tree inference in presence of hybridization and undetected paralogy or other causes leading to extremely discordant gene trees.
|
|
| 31. |
- Tinetti, G., et al.
(författare)
-
A chemical survey of exoplanets with ARIEL
- 2018
-
Ingår i: Experimental Astronomy. - : Springer Science and Business Media LLC. - 0922-6435 .- 1572-9508. ; 46:1, s. 135-209
-
Tidskriftsartikel (refereegranskat)abstract
- Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.
|
|
| 32. |
- Witjes, J. Alfred, et al.
(författare)
-
EAU-ESMO Consensus Statements on the Management of Advanced and Variant Bladder Cancer – An International Collaborative Multistakeholder Effort : Under the Auspices of the EAU-ESMO Guidelines Committees
- 2020
-
Ingår i: European Urology. - : Elsevier. - 0302-2838 .- 1873-7560. ; 77:2, s. 223-250
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Although guidelines exist for advanced and variant bladder cancer management, evidence is limited/conflicting in some areas and the optimal approach remains controversial.OBJECTIVE: To bring together a large multidisciplinary group of experts to develop consensus statements on controversial topics in bladder cancer management.DESIGN: A steering committee compiled proposed statements regarding advanced and variant bladder cancer management which were assessed by 113 experts in a Delphi survey. Statements not reaching consensus were reviewed; those prioritised were revised by a panel of 45 experts prior to voting during a consensus conference.SETTING: Online Delphi survey and consensus conference.PARTICIPANTS: The European Association of Urology (EAU), the European Society for Medical Oncology (ESMO), experts in bladder cancer management.OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Statements were ranked by experts according to their level of agreement: 1-3 (disagree), 4-6 (equivocal), and 7-9 (agree). A priori (level 1) consensus was defined as ≥70% agreement and ≤15% disagreement, or vice versa. In the Delphi survey, a second analysis was restricted to stakeholder group(s) considered to have adequate expertise relating to each statement (to achieve level 2 consensus).RESULTS AND LIMITATIONS: Overall, 116 statements were included in the Delphi survey. Of these statements, 33 (28%) achieved level 1 consensus and 49 (42%) achieved level 1 or 2 consensus. At the consensus conference, 22 of 27 (81%) statements achieved consensus. These consensus statements provide further guidance across a broad range of topics, including the management of variant histologies, the role/limitations of prognostic biomarkers in clinical decision making, bladder preservation strategies, modern radiotherapy techniques, the management of oligometastatic disease, and the evolving role of checkpoint inhibitor therapy in metastatic disease.CONCLUSIONS: These consensus statements provide further guidance on controversial topics in advanced and variant bladder cancer management until a time when further evidence is available to guide our approach.PATIENT SUMMARY: This report summarises findings from an international, multistakeholder project organised by the EAU and ESMO. In this project, a steering committee identified areas of bladder cancer management where there is currently no good-quality evidence to guide treatment decisions. From this, they developed a series of proposed statements, 71 of which achieved consensus by a large group of experts in the field of bladder cancer. It is anticipated that these statements will provide further guidance to health care professionals and could help improve patient outcomes until a time when good-quality evidence is available.
|
|
